Receptor
PDB id Resolution Class Description Source Keywords
5APG 1.6 Å EC: 2.5.1.- STRUCTURE OF THE SAM-DEPENDENT RRNA:ACP-TRANSFERASE TSR3 FROM VULCANISAETA DISTRIBUTA VULCANISAETA DISTRIBUTA TRANSFERASE S-ADENOSYLMETHIONINE S-ADENOSYLMETHIONINE DEPE3-AMINO-3-CARBOXYPROPYL TRANSFERASE RRNA PSEUDOURIDINE SSPOUT-FOLD
Ref.: RIBOSOME BIOGENESIS FACTOR TSR3 IS THE AMINOCARBOXY TRANSFERASE RESPONSIBLE FOR 18S RRNA HYPERMODIFICAT YEAST AND HUMANS NUCLEIC ACIDS RES. V. 44 4304 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EEM B:1185;
C:1185;
A:1185;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
446.34 C15 H23 N6 O5 Se C[Se@...
MES B:1186;
A:1187;
A:1186;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
195.237 C6 H13 N O4 S C1COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5APG 1.6 Å EC: 2.5.1.- STRUCTURE OF THE SAM-DEPENDENT RRNA:ACP-TRANSFERASE TSR3 FROM VULCANISAETA DISTRIBUTA VULCANISAETA DISTRIBUTA TRANSFERASE S-ADENOSYLMETHIONINE S-ADENOSYLMETHIONINE DEPE3-AMINO-3-CARBOXYPROPYL TRANSFERASE RRNA PSEUDOURIDINE SSPOUT-FOLD
Ref.: RIBOSOME BIOGENESIS FACTOR TSR3 IS THE AMINOCARBOXY TRANSFERASE RESPONSIBLE FOR 18S RRNA HYPERMODIFICAT YEAST AND HUMANS NUCLEIC ACIDS RES. V. 44 4304 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5APG - EEM C15 H23 N6 O5 Se C[Se@@+](C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5APG - EEM C15 H23 N6 O5 Se C[Se@@+](C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5APG - EEM C15 H23 N6 O5 Se C[Se@@+](C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: EEM; Similar ligands found: 249
No: Ligand ECFP6 Tc MDL keys Tc
1 EEM 1 1
2 SA8 0.625 0.945205
3 SFG 0.62069 0.875
4 SAH 0.617977 0.890411
5 S7M 0.608696 0.894737
6 5X8 0.602273 0.863014
7 SAI 0.6 0.930556
8 0UM 0.583333 0.857143
9 62X 0.561224 0.884615
10 ADN 0.558442 0.773333
11 XYA 0.558442 0.773333
12 RAB 0.558442 0.773333
13 SMM 0.557895 0.909091
14 5CD 0.556962 0.783784
15 K15 0.555556 0.883117
16 DTA 0.548781 0.766234
17 M2T 0.548781 0.828947
18 5N5 0.544304 0.773333
19 SAM 0.542553 0.945946
20 MTA 0.542169 0.849315
21 A4D 0.5375 0.773333
22 EP4 0.536585 0.826667
23 3DH 0.529412 0.824324
24 KB1 0.524272 0.833333
25 5AL 0.520833 0.743902
26 AMO 0.52 0.746988
27 ME8 0.514563 0.819277
28 6RE 0.511364 0.78481
29 A3S 0.51087 0.813333
30 SRP 0.510204 0.746988
31 KYE 0.509434 0.802469
32 DSZ 0.504951 0.666667
33 KH3 0.504587 0.871795
34 KXW 0.504587 0.844156
35 NWW 0.5 0.739726
36 A 0.5 0.707317
37 KG4 0.5 0.714286
38 ABM 0.5 0.753086
39 45A 0.5 0.753086
40 LMS 0.5 0.630435
41 5CA 0.5 0.648936
42 AMP 0.5 0.707317
43 SXZ 0.5 0.87013
44 ZAS 0.5 0.769231
45 A5A 0.5 0.652174
46 Q2M 0.495575 0.822785
47 8QN 0.49505 0.743902
48 SSA 0.494949 0.648936
49 8LH 0.494949 0.746988
50 SON 0.494624 0.746988
51 AN2 0.494624 0.682353
52 A7D 0.494624 0.826667
53 GJV 0.494505 0.775
54 S4M 0.494505 0.860759
55 AMP MG 0.494382 0.7375
56 EU9 0.491071 0.767442
57 GSU 0.490385 0.684783
58 LAD 0.490385 0.752941
59 PAJ 0.490196 0.712644
60 LSS 0.490196 0.670213
61 54H 0.49 0.638298
62 VMS 0.49 0.638298
63 8LE 0.489796 0.717647
64 CA0 0.489362 0.714286
65 MAO 0.48913 0.82716
66 DSH 0.488889 0.818182
67 HZ2 0.486486 0.822785
68 DAL AMP 0.485149 0.765432
69 8LQ 0.485149 0.768293
70 53H 0.485149 0.631579
71 TSB 0.485149 0.645161
72 G5A 0.484536 0.648936
73 A3T 0.484211 0.8
74 5AS 0.483871 0.614583
75 J7C 0.483516 0.772152
76 A2D 0.483516 0.690476
77 OZP 0.482143 0.844156
78 GEK 0.480392 0.88
79 9ZA 0.480392 0.729412
80 9ZD 0.480392 0.729412
81 V47 0.48 0.810811
82 0XU 0.479167 0.824324
83 HY8 0.477876 0.822785
84 SRA 0.477778 0.674419
85 KAA 0.47619 0.663158
86 52H 0.475248 0.631579
87 5AD 0.475 0.75
88 V2G 0.474747 0.701149
89 M33 0.473684 0.722892
90 N37 0.473684 0.828947
91 ADX 0.473684 0.630435
92 A12 0.473118 0.705882
93 AP2 0.473118 0.705882
94 BA3 0.473118 0.690476
95 NEC 0.472527 0.75
96 A3G 0.472527 0.802632
97 AOC 0.472527 0.776316
98 PTJ 0.471698 0.72093
99 NB8 0.471698 0.72093
100 TXA 0.471698 0.72619
101 AHX 0.471154 0.701149
102 NVA LMS 0.471154 0.698925
103 QA7 0.470588 0.738095
104 Y3J 0.46988 0.706667
105 F0P 0.469565 0.844156
106 Q34 0.469565 0.802469
107 50T 0.46875 0.702381
108 AP5 0.468085 0.690476
109 ADP 0.468085 0.690476
110 B4P 0.468085 0.690476
111 A3N 0.467391 0.766234
112 LEU LMS 0.466667 0.714286
113 GAP 0.464646 0.73494
114 PRX 0.463918 0.73494
115 AT4 0.463158 0.666667
116 ADP MG 0.463158 0.728395
117 ADP BEF 0.463158 0.728395
118 F2R 0.462185 0.7
119 4AD 0.461538 0.759036
120 NWQ 0.460674 0.767123
121 AAT 0.46 0.775
122 AD9 0.459184 0.694118
123 A5D 0.459184 0.766234
124 FA5 0.458716 0.746988
125 MHZ 0.458333 0.82716
126 AU1 0.458333 0.674419
127 9K8 0.457944 0.628866
128 Q2V 0.457627 0.833333
129 YLC 0.456897 0.755814
130 YLB 0.456897 0.758621
131 YLP 0.45614 0.738636
132 U4Y 0.45614 0.855263
133 3AM 0.455556 0.674699
134 7MD 0.455357 0.715909
135 VRT 0.454545 0.842105
136 XAH 0.454545 0.715909
137 ATP 0.453608 0.690476
138 HEJ 0.453608 0.690476
139 H1Q 0.453608 0.740741
140 ACP 0.453608 0.694118
141 S8M 0.451923 0.807692
142 7D7 0.451219 0.723684
143 AR6 0.44898 0.710843
144 APC 0.44898 0.705882
145 5FA 0.44898 0.690476
146 APR 0.44898 0.710843
147 AQP 0.44898 0.690476
148 WAQ 0.448598 0.75
149 3NZ 0.448598 0.807692
150 NSS 0.447619 0.666667
151 TT8 0.446602 0.917808
152 Q2P 0.446281 0.802469
153 ATP MG 0.444444 0.728395
154 AGS 0.444444 0.659091
155 APC MG 0.444444 0.731707
156 ADV 0.444444 0.72619
157 RBY 0.444444 0.72619
158 ADP PO3 0.444444 0.728395
159 00A 0.443396 0.689655
160 ARG AMP 0.442478 0.727273
161 D3Y 0.442308 0.792208
162 8X1 0.442308 0.645833
163 YSA 0.441441 0.648936
164 N5O 0.44086 0.789474
165 BEF ADP 0.44 0.731707
166 3UK 0.439252 0.714286
167 OAD 0.439252 0.73494
168 80F 0.439024 0.681319
169 2VA 0.438776 0.779221
170 QXP 0.438095 0.634409
171 5SV 0.438095 0.741176
172 OOB 0.438095 0.722892
173 IOT 0.436975 0.711111
174 9SN 0.436364 0.681818
175 TAT 0.435644 0.666667
176 ANP 0.435644 0.674419
177 ACQ 0.435644 0.694118
178 T99 0.435644 0.666667
179 R2V 0.435185 0.634409
180 B5V 0.435185 0.705882
181 J4G 0.435185 0.759036
182 A1R 0.433962 0.709302
183 HQG 0.432692 0.702381
184 B5M 0.432432 0.717647
185 B5Y 0.432432 0.717647
186 8PZ 0.432432 0.648936
187 N5A 0.431579 0.786667
188 BIS 0.431193 0.670455
189 1ZZ 0.431193 0.755814
190 3OD 0.431193 0.73494
191 48N 0.431034 0.72093
192 NVA 2AD 0.43 0.855263
193 DLL 0.429907 0.722892
194 AYB 0.429752 0.75
195 A22 0.428571 0.682353
196 MAP 0.428571 0.678161
197 2AM 0.428571 0.666667
198 MYR AMP 0.427273 0.776471
199 VO4 ADP 0.427184 0.714286
200 ATF 0.427184 0.666667
201 ANP MG 0.427184 0.702381
202 ALF ADP 0.427184 0.697674
203 A3P 0.427083 0.686747
204 A6D 0.425926 0.705882
205 QXG 0.425926 0.62766
206 9X8 0.425926 0.697674
207 SO8 0.425743 0.792208
208 TYM 0.423729 0.746988
209 6YZ 0.423077 0.694118
210 P5A 0.422018 0.65625
211 PR8 0.422018 0.744186
212 YLA 0.421488 0.719101
213 7C5 0.421053 0.731707
214 A3R 0.420561 0.709302
215 RP1 0.419355 0.651163
216 SP1 0.419355 0.651163
217 FYA 0.418182 0.722892
218 7D5 0.417582 0.658824
219 JNT 0.416667 0.694118
220 K2H 0.416667 0.805195
221 KY2 0.415094 0.777778
222 KY5 0.414414 0.818182
223 4YB 0.413793 0.670213
224 2BA 0.412371 0.682927
225 CMP 0.412371 0.691358
226 WSA 0.411765 0.655914
227 OZV 0.411215 0.690476
228 25A 0.411215 0.690476
229 AHZ 0.410256 0.735632
230 K2K 0.409091 0.807692
231 7MC 0.408333 0.719101
232 KYB 0.407407 0.777778
233 ADQ 0.407407 0.694118
234 YLY 0.40625 0.770115
235 JB6 0.405405 0.689655
236 QQY 0.404255 0.627907
237 PPS 0.403846 0.612903
238 B1U 0.403509 0.6
239 K3H 0.403509 0.775
240 NAI 0.403361 0.670455
241 PAP 0.401961 0.678571
242 TAD 0.401709 0.693182
243 DQV 0.401709 0.702381
244 OVE 0.4 0.643678
245 ADP BMA 0.4 0.714286
246 4UV 0.4 0.697674
247 ALF ADP 3PG 0.4 0.732558
248 OMR 0.4 0.747126
249 AF3 ADP 3PG 0.4 0.732558
Similar Ligands (3D)
Ligand no: 1; Ligand: EEM; Similar ligands found: 3
No: Ligand Similarity coefficient
1 GDP 0.8812
2 GTP 0.8762
3 M7G 0.8588
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5APG; Ligand: EEM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5apg.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5APG; Ligand: EEM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5apg.bio3) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5APG; Ligand: EEM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5apg.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
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